QTL mapping of fire blight resistance in apple is an effective tool to determine associations between regions in the genome of apple and resistance to the bacterial disease. Several wild Malus accessions of different apple species have been identified as resistant to fire blight making them valuable as donors for the introgression of resistance to the cultivated apple Malus × domestica Borkh. Resistant accessions of the wild species M. baccata, M. fusca and M. × robusta 5 (Mr5) were inoculated with the wild type strain Ea1189 and the AvrRpt2EA deletion mutant (pZYRKD3-1). While M. baccata and M. fusca showed no symptoms to pZYRKD3-1, the resistance of M. × robusta 5 was overcome by pZYRKD3-1 with an average necrosis length of 52% respectively. Inoculation of the mapping population ‘Idared’ × Mr5 with the strain Ea 1189 results in the confirmation of the QTL on LG 3 in Mr5; this QTL completely broke down after inoculation with pZYRKD3-1, but two minor QTLs on LG 7 and LG 11 were detected.